Lab 8 Learning Objectives

• Prepare a simple R package for distributing documented functions

• Explain the terms Repository, Dependency, and Namespace

• Implement testing in an R package

• Collaboratively work on an R package on GitHub

What is an R package?

• A shareable collection of documented code and/or data

The package you built

DESCRIPTION

Imports vs Depends

Package: PackageName
Type: Package
Title: Central Dogma
Version: 0.1.0
Description: simple R package that replicates the central dogma of molecular biology.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: 
    ggplot2,
    stringr
Depends:
    R (>= 4.0)

Missing DESCRIPTION

> ?randomDNA
ℹ Rendering development documentation for "randomDNA"
Error in .get_package_metadata(pkgdir) : 
  Files 'DESCRIPTION' and 'DESCRIPTION.in' are missing.
Error in .get_package_metadata(pkgdir) : 
  Files 'DESCRIPTION' and 'DESCRIPTION.in' are missing.

The NAMESPACE file

> devtools::document()
ℹ Updating cdogma documentation
ℹ Loading cdogma
Warning message:
Skipping NAMESPACE
✖ It already exists and was not generated by roxygen2.

The NAMESPACE file

# Generated by roxygen2: do not edit by hand

<<<<<<< HEAD
export(function_x)
=======
export(function_y)
>>>>>>> e34c9e2848142b2afa6394733438e78434483ebc

Failing devtools::check()

❯ checking examples ... ERROR
  Running examples in ‘cdogma-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: hello
  > ### Title: Hello, World!
  > ### Aliases: hello
  > 
  > ### ** Examples
  > 
  > hello()
  Error in hello() : could not find function "hello"
  Execution halted

Group assignment

• Make an R package that simulate (more or less) the central dogma of molecular biology.
• Discuss why it is a good idea to limit the number of dependencies your package has. When can’t it be avoided?
• Discuss the difference between adding an @importFrom package function tag to a function description compared to using package::function().
• Write a vignette (user guide)

Package names

• centralDogma / Centraldog / cdogma / centdog / Cdogr
• enigma
• molecbio
• dogmaVis
• BioFlow
• BioSeqR
• gene2protein
• biocd / AnalysisCD
• CDXX / dogmaXX / groupXX

Dependencies

• They increase the size of our package.

• Can introduce compatibility issues.

• They are rarely avoidable.

Namespace

• Extent your package’s namespace with dependency imports
  • @importFrom package function and @import package
  • Cannot be replaced by package::function
  • What is actually the difference?
• package::function…
  • clutters the code…
  • and can be tiresome if used heavily…
  • but ensure better understanding.